WASHINGTON — In the weeks after President Trump chose John R. Bolton to be his third national security adviser in March, Mr. Bolton, a veteran of the George W. Bush State Department whose bellicose manner kept him from a high-level job at the beginning of the Trump administration, engaged in his own sped-up transition process, aided by a handful of longtime associates.

Drawn from the world of conservative politics, international consulting and defense contracting, and working out of the downtown Washington offices of Mr. Bolton’s political organizations, the group of advisers provided advice on National Security Council operations, while helping to vet prospective new hires for views that would be compatible with his own.

Nearly two months into Mr. Bolton’s tenure, some people familiar with the National Security Council say the influence of his associates can be seen in the agency’s effort to crack down on leaks, as well as an exodus of agency staff members and a roster of candidates now under consideration to take their place, and have taken to calling the associates a “shadow N.S.C.”

One of Mr. Bolton’s longtime associates, Charles M. Kupperman, a former Reagan administration official and defense contracting executive, has taken a temporary leadership post on the National Security Council, while at least three others — Frederick H. Fleitz, Sarah Tinsley and David Wurmser — are believed to be under consideration for posts.

Mr. Bolton’s relationships with most of the associates date back decades, to his days working in positions related to foreign policy in the Reagan administration. But he continued working with them in the dozen years since he has been out of government, serving as an adviser to Mr. Wurmser’s company, according to its website, while relying on Mr. Kupperman, Ms. Tinsley and several other associates to help run a constellation of conservative political organizations that he founded to advance his foreign policy views and political prospects.

The activity brought Mr. Bolton into regular contact with some of the biggest donors on the right, while giving him a platform to explore his own possible presidential campaign in 2016 and to be an advocate for confrontational strategies in dealing with Iran, North Korea and Russia.

Mr. Bolton’s continued reliance on longtime associates in either informal or temporary capacities at the National Security Council has raised concerns among government watchdog organizations and agency veterans and scholars. They say it creates questions of conflicts of interest and an echo chamber of identical views with little room for dissent at the agency charged with coordinating policy throughout the government’s military, foreign policy and intelligence communities and synthesizing the best advice for the president.

“Very much like the president, Bolton has picked a small coterie of people from past lives who look more like cronies and buddies than they do the array of senior experts on different issues that past national security advisers have brought in,” said David J. Rothkopf, a former Clinton administration official who wrote a definitive history of the National Security Council.

Rather than fulfilling Mr. Trump’s promise that he would fill his administration with “the best people,” Mr. Rothkopf said, the president has got “this highly controversial national security adviser who has never crossed a bridge he hasn’t burned behind him, who is surrounding himself with what appears to be a second-tier group of advisers who have spent a disproportionate amount of time on the swamp side of things — as consultants or working on his extreme political projects.”

People familiar with Mr. Bolton’s cadre of advisers say that arguably the most influential among them is a low-profile 64-year-old consultant named Matthew C. Freedman, who has been close to Mr. Bolton since the two met in the early 1980s at the United States Agency for International Development, and over time has taken on the role of unofficial chief of staff in Mr. Bolton’s government and political ventures.

After his early foray in government, Mr. Freedman went on to become a foreign lobbyist working with Paul Manafort in the 1980s and 1990s for sometimes unsavory but well-paying foreign leaders, including Ferdinand Marcos, the Philippine strongman. Yet Mr. Freedman continued weaving in and out of part-time or temporary government jobs while also running a consulting firm, Global Impact Inc., that advertises on its website the ability to help governments and companies with “international security and multilateral diplomacy,” among other areas.

More recently, Mr. Freedman served on the Trump transition team, but he was fired in late 2016 for using an email address associated with his consulting firm to conduct government business, raising concerns that he was using the position to boost his business.

Mr. Freedman interviewed prospective N.S.C. hires from Mr. Bolton’s Washington political office and reviewed information provided by the National Security Council about its structure, while providing advice to Mr. Bolton about prospective hires and changes, according to people familiar with the arrangement.

They said that Mr. Freedman was seen as an advocate for wide-scale firings at the agency — which he has denied — and that he has advised Mr. Bolton to fill top jobs with more longtime, close associates from their circle, several of whom are being considered.

Politico first reported Mr. Freedman’s role in screening prospective agency hires on Sunday.

While serving as an informal adviser, Mr. Freedman continued working as a subcontract consultant with the United States Navy and a special government employee with the United States Army, while also running Global Impact.

Mr. Freedman has no formal role with the National Security Council, but he still talks about matters related to the agency with Mr. Bolton and Mr. Kupperman, who took a temporary job as a senior adviser to the National Security Council at a rate of $78.67 an hour; he is expected to leave early next month. Meanwhile, Global Impact’s website has continued to list Mr. Kupperman as an adviser to the company, though people familiar with the arrangement say Mr. Kupperman is not paid by the firm.

Robert Palladino, a spokesman for the National Security Council, defended the role played by Mr. Freedman and Mr. Kupperman, and said they performed an invaluable service for Mr. Bolton as he was assuming the leadership of the agency by helping him sort through more than 500 résumés from people interested in working for the agency.

“Consulting with trusted colleagues, such as Mr. Freedman and Dr. Kupperman, not only makes practical sense, it also makes strategic sense, as Dr. Kupperman and Mr. Freedman both share a conviction to which Ambassador Bolton subscribes: ‘Peace Through Strength,’” Mr. Palladino said in a statement.

He added that “no classified information was ever provided to Mr. Freedman” while he worked from Mr. Bolton’s political office. “The information shared with Mr. Freedman was downloaded from public websites or created from publicly available information.”

But Walter M. Shaub Jr., who resigned as the head of the Office of Government Ethics after repeatedly calling out the Trump administration for ethical lapses, said it could be ethically charged to have consultants who do business with the government “moonlighting” as advisers to Mr. Bolton.

He pointed out that unofficial advisers like Mr. Freedman are not covered by conflict-of-interest rules. And even though temporary employees like Mr. Kupperman are covered by ethics rules and are required to disclose their outside interests to their agencies, those disclosures are not made public.

The lack of transparency “means we have no way of knowing whether these individuals are accessing information that could prove useful for their own private government consulting activities,” Mr. Shaub said.

Also complicating Mr. Bolton’s transition back into government has been the network of advocacy groups Mr. Bolton championed that are linked to major donors, political figures and interest groups seeking to influence the Trump administration’s foreign policy.

Ms. Tinsley, Mr. Marquis and Christine Samuelian, a longtime assistant to Mr. Bolton who has joined him as an aide at the National Security Council, also helped run a pair of political action committees fronted by Mr. Bolton that have raised more than $24 million since 2013 — including $5 million from the hedge fund magnate Robert Mercer — to support hawkish candidates.

Campaign finance reportsfiled Sunday show that the committees paid nearly $16,000 in payroll to Ms. Tinsley, who first worked with Mr. Bolton at the United States Agency for International Development, and nearly $8,700 to Ms. Samuelian last month after Mr. Bolton assumed his office at the National Security Council, though the PACs had already largely suspended operations and the payments were most likely postdated.

Mr. Bolton is also close to the Republican megadonor Sheldon G. Adelson, an influential hawk and supporter of Israel from whom Mr. Bolton has sought assistance for his political ventures. Mr. Adelson, a casino billionaire, urged the Trump administration to hire Mr. Bolton for a senior post, according to someone familiar with the relationship, and also urged Mr. Trump to withdraw from the Iran deal. The day after Mr. Trump announced he was doing just that, Mr. Adelson attended a private meeting at the White House with Mr. Trump, Vice President Mike Pence, Treasury Secretary Steven Mnuchin and Mr. Bolton, though someone familiar with the meeting said it had been long planned and was unrelated to the announcement.

After Mr. Bolton was named national security adviser, Ms. Tinsley worked with him to wind down the political groups, while Mr. Marquis, a communications consultant who is a partner in a firm that has lobbied on behalf of foreigncompanies and one country, Japan, helped Mr. Bolton with public relations, reaching out to reporters to push back on critical stories and social media posts.

Mr. Marquis, 35, and Ms. Tinsley, 64, declined to comment. So did Mr. Freedman; Mr. Fleitz, 56, a former chief of staff to Mr. Bolton when he was under secretary for arms control in President George W. Bush’s administration; and Mr. Wurmser, 56, who served as a special assistant to Mr. Bolton in the Bush State Department and also as an aide to Vice President Dick Cheney.

Mr. Palladino stressed that the overwhelming majority of National Security Council staff members are career government employees detailed from the military, foreign service, Civil Service and intelligence agencies, and he said there has been relatively little turnover in those positions.

“These subject-matter experts will continue to serve the new national security adviser in support of the president’s national security objectives,” he said, adding that their presence will help ensure that “for any given national security issue, the president is provided with a full range of options.”

But Max Stier, the head of the Partnership for Public Service, a nonpartisan nonprofit that studies the federal work force, said that changes in personnel and approach accompanying each new leadership circle at the National Security Council “create real risk for our country because of the lack of continuity.”

Under previous presidents, he said, “You see this happening at the beginning of an administration. You just don’t see this happening three times in the first 16 months.”

A version of this article appears in print on , on Page A13 of the New York edition with the headline: Bolton Is Relying on ‘Shadow N.S.C.’ of His Allies, Worrying Watchdogs. Order Reprints | Today’s Paper | Subscribe